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How To Get Genbank File Using Bioperl

I currently have the following:

use Bio::SeqIO;

$seqio_obj = Bio::SeqIO->new(-file => "J01673.gb", -format => "genbank" );
$seq_obj = $seqio_obj->next_seq;

I am not able to get output using above code.

bioperl
• 4,584 views • link
updated by Biostar Biostar • written by shilpy • shilpy

That's because none of that code generates any output.

• 36 views • link
written by Neilfws Neilfws

Have you already downloaded the file J01673.gb or are you trying to get BioPerl to download it for you? See Hernan's reply below.

• 0 views • link
written by Peter Peter

1 answer

May be something like:

use Bio::DB::GenBank;
$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' , -format => 'gb');
$seqio_object = $gb->get_Stream_by_id(['J00522']);
while( my $seq = $seqio_object->next_seq ) {
    $seqio_object->write_seq($seq);}
• 211 views • link
written by Hernán Hernán

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